Without using terminal, you can drag your files from the origin folder (AeroFS Backup) to the destination folder (AeroFS) and when Finder realizes that the same file exists, it will show an alert, asking you what you want it to do. If you press "Option" while looking at that alert, one of the options will change to "Skip" and you can then apply that to all the files that you are dragging over.

I recorded a brief video showing this in action

Without using terminal, you can drag your files from the origin folder (AeroFS Backup) to the destination folder (AeroFS) and when Finder realizes that the same file exists, it will show an alert, asking you what you want it to do. If you press "Option" while looking at that alert, one of the options will change to "Skip" and you can then apply that to all the files that you are dragging over.

I recorded a brief video showing this in action

Using Terminal, I highly recommend the RSYNC solution:

rsync -av --ignore-existing sourceFolder/ destinationFolder